Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a "lab-on-a-molecule" prototype

We demonstrate the first three-input molecular AND logic gate based on three chemical inputs as a direct way of detecting congregations of chemical species. The AND gate operates in water and responds to Na+, H+, and Zn2+ inputs with an enhanced fluorescence signal when pre-set concentration thresholds are exceeded. Future "lab-on-a-molecule" devices could have application in medicine for rapid disease screening.     

The solvent effect on a styryl-bodipy derivative functioning as an AND molecular logic gate

We study via DFT and TDDFT calculations the photophysical processes of a styryl-bodipy derivative, ( 1 ), of its monometallic complexes 1-M ²⁺ (M = Ca, Zn, and Hg), and its trimetallic complex ( 2 ) unprotonated, protonated and complexed with water molecules in water solvent and in acidic conditions. The main targets of this study are to gain information regarding published reports on fluorophore species mentioning that fluorescent switching results from trace water, to study how 1 behaves in water solvent which is a common used solvent for molecular logic gates (MLG), and how it behaves in acidic conditions. We conclude that in water solvent, as in acetonitrile solvent (which was found before both theoretically and experimentally) there will be a quenching of emission spectra in 1 and 1-M ²⁺ and a retaining of emission in 2 . However, contrary to acetonitrile solvent, in water, a weak peak will be observed for 1 and 1-M ²⁺ , due to a small ratio of reversible protonation, showing that in acetonitrile 1 acts as a better MLG candidate than in water solvent. On the other hand, in acidic conditions all five species will emit and as a result, 1 will not be an AND MLG, showing that the selection of the solvent conditions is crucial for a species to act as an MLG candidate. Finally, we conclude that the retaining of emission is accomplished by the simultaneous tetrahedral geometry of all three aniline N atoms.     

A fluorescent molecular logic gate with multiply-configurable dual outputs

A simple molecule, L, diethylenetriamine bearing anthracene fragments at both ends, behaves as a fluorescent molecular logic gate with "multiply-configurable dual outputs", capable of demonstrating five different logic functions operated by proton (H+) and transition metal cations (Mn+) as inputs.     

Theoretical study of the photophysical processes of a styryl-bodipy derivative eliciting an AND molecular logic gate response

We study, via density functional theory and time dependent DFT calculations, the photophysical processes of a styryl-bodipy derivative, which acts as a three metal-cation-receptor fluorophore in order to (a) gain information on the appropriate computational approach for successful prediction of molecular logic gate candidates, (b) rationalize the available experimental data and (c) understand how the given combination of three different receptors with the BODIPY fluorophore presents such interesting optoelectronic responses. The fluorophore ( 1 ), its monometallic complexes ( 1-Ca ²⁺ , 1-Zn ²⁺ , and 1-Hg ²⁺ ), and its trimetallic complex ( 2 ) are studied. The calculated λ_max values for absorption and emission are in excellent agreement with experimental data. It was found that the observed quenching of emission of 1 and of the monometallic complexes is attributed to the fact that their first excited state is a charge-transfer state whereas this does not happen for the complex 2 . It should be noted that for the correct ordering of the excited states, the inclusion of corrections to the excitation energies for nonequilibrium solvent effects is required; while in the case of 1-Ca ²⁺ , the additional explicit inclusion of the solvent is necessary for the quenching of the emission spectra.     

Benzimidazole-based ratiometric fluorescent receptor exhibiting molecular logic gate for Cu and Fe

We synthesized a novel fluorescent receptor based upon a benzimidazole moiety in a dipodal framework. The receptor exhibited a dual fluorescence emission which is quenched upon addition of Cu²⁺ or Fe³⁺. Interestingly, the receptor offers a ratiometric property and an ‘OR’ logic gate property to Cu²⁺ and Fe³⁺.     

Fluorescent polymeric AND logic gate with temperature and pH as inputs

We illustrate a general polymeric design of fluorescent logic gates, for example, AND, using temperature and pH as inputs.     

A triethylenetetramine bearing anthracene and benzophenone as a fluorescent molecular logic gate with either-or switchable dual logic functions

Fluorescence behaviors of a triethylenetetramine bearing anthracene (AN) and benzophenone (BP) fragments at the respective ends, L1, have been studied in water, where effects of pH (H+) and metal cations on the emission properties have been studied in detail. L1 behaves as a fluorescent molecular logic gate driven by H+ (Input1) and metal cations (Input2) as input chemicals. The most notable feature of L1 is that this molecule expresses the "either-or" switchable dual logic functions. Operation of L1 with Cu2+ as Input2 expresses the INHIBIT logic function, where a strong AN fluorescence appears only at pH 4 (with H+) without Cu2+ [Input1(1)-Input2(0)]. In contrast, operations of L1 with all other metal cations as Input2 express the TRANSFER logic function, where the presence of H+ allows strong AN fluorescence regardless of whether the metal cation exists or not [Input1(1)-Input2(0); Input1(1)-Input2(1)]. These emission switching behaviors of L1 are driven by the difference in the coordination stability between L1 and metal cations and the photoinduced intramolecular electron and energy transfer processes: (i) a pH-induced electron transfer from unprotonated nitrogen atoms of the polyamine chain to the photoexcited AN [ELT(N-->AN*)]; (ii) a pH- and metal coordination-induced electron transfer from the photoexcited AN to the ground-state BP [ELT(AN*-->BP)]; and (iii) a Cu2+ coordination-induced energy transfer from the photoexcited AN to Cu2+ [ENT(AN*-->Cu2+)].     

l-Arginine bearing an anthrylmethyl group: fluorescent molecular NAND logic gate with H and ATP as inputs

A novel l-arginine derivative was synthesized and its interactions with ATP in aqueous solutions were demonstrated by fluorescence, UV-vis, and ¹H NMR spectroscopy. A two-input NAND logic gate was presented on the basis of this single molecule.     

Consolidating molecular AND logic with two chemical inputs

A novel molecular AND logic gate 1 is demonstrated based on the competition between fluorescence and photoinduced electron transfer (PET). It is constructed according to a 'receptor2-spacer-fluorophore-spacer-receptor1-spacer-fluorophore-spacer-receptor2' format where receptor1 is a tertiary amine, receptor2 is a benzo-15-crown-5 ether and the fluorophore is an anthracene moiety, which are separated from each other by methylene spacers. The fluorescence response in methanol is significantly enhanced only when both H+ and Na+ are the inputs at high enough concentrations in accordance with AND logic. Cs+ behaves similarly to Na+, but with a lower fluorescence enhancement, whereas the other alkali metal cations are not effective. Electrospray ionization mass spectrometry provides evidence for formation of 1:1 and 1:2 (1:metal) complexes with alkali cations, and formation of a 1:2:1 (1:metal:proton) complex in the additional presence of acid.     

Accelerated molecular dynamics simulations of protein folding

Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred‐of‐microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2–2.1 Å of the native NMR or X‐ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second‐order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein‐folding studies. © 2015 Wiley Periodicals, Inc.     

Design of a DNA electronic logic gate (INHIBIT gate) with an assaying application for Ag+ and cysteine

A DNA electronic logic gate (INHIBIT gate) with good selectivity and reversibility is developed based on using Ag(+) and Cys as inputs and current signal as output.     

Tuning the CD spectrum and optical rotation value of a new binaphthalene molecule with two spiropyran units: mimicking the function of a molecular "AND" logic gate and a new chiral molecular switch

With the view to developing new chiral molecular switches and logic gates, a new binaphthalene molecule with two spiropyran units (1) was synthesized and characterized. Absorption and 1H NMR spectral studies of 1 after reaction with acid/base indicate acidichromism can occur to compound 1. The synergistic actions of acid and UV light irradiation result in a remarkable change for the CD spectrum of the relatively dilute solution of 1, mimicking the behavior of a chiral "AND" gate, since the "ouput" is the CD signal. Furthermore, the optical rotation value of the relatively concentrated solution of 1 can be reversibly tuned after sequential reactions with acid and base, and thus a chiral molecular switch with nondestructive "output" signal is realized. The present results not only add a new example of chiral molecular switch with nondestructive readout but also provide a chiral "AND" gate based on the axial chiral binaphthalene to which switchable units are linked.     

A new tetrathiafulvalene-anthracence dyad fusion with the crown ether group: fluorescence modulation with Na+ and C60, mimicking the performance of an "AND" logic gate

In this Note, we describe a new TTF-anthracene dyad fusion with the crown ether unit. It is interesting to find that the fluorescence of this new dyad can be modulated with Na+ and C60, and its fluorescence intensity can be largely enhanced only in the presence of both Na+ and C60. Such fluorescence modulation behavior mimics the performance of a two-input "AND" logic gate.     

AND logic gate application based on colorimetric screening of enzyme activity

A simple and novel DNA and gold nanoparticle (AuNPs) based colorimetric method has been developed for efficient detection of Deoxyribonuclease I (DNase-I) activity. For the detection process, the sample that contains DNase-I, which will cleave double stranded DNA into small pieces. Furthermore, the small pieces DNA sequences and water-soluble conjugated polymer cause the AuNPs aggregation (the solution change the color from red to blue). Thus, DNase-I could be detected by naked eyes or UV/Vis. Molecular substrates can be viewed as computational devices that process physical or chemical ‘inputs’ to generate ‘outputs’ based on a set of logical operators. Based on the assay, we have presented a DNA/AuNP based, multi-readout AND logic operations.     

Assessment of protein folding potentials with an evolutionary method

Many different protein folding potentials have been developed in the last decades, based upon knowledge of experimentally determined protein structures. Decoy-based techniques are frequently used to assess these force fields, but other methods can explore different features in the performance of the interaction schemes, thus helping in their evaluation. Here, we propose an evolutionary strategy to efficiently assess folding potentials. We apply it to three potentials with different characteristics, taken from the bibliography. A search for minimum energy protein topologies, treated as arrangements of rigid protein fragments, is performed. The method, applied to a set of helix bundle proteins, shows the different behavior of the studied potentials, providing a reasonably fast tool to evaluate their advantages and limitations.     

Oscillatory molecular driving force for protein folding at high concentration: a molecular simulation

This paper presents a Langevin dynamics simulation that suggests a novel way to fold protein at high concentration, a fundamental issue in neurodegenerative diseases in vivo and the production of recombinant proteins in vitro. The simulation indicates that the folding of a coarse-grained beta-barrel protein at high concentration follows the "collapse-rearrangement" mechanism but it yields products of various forms, including single proteins in the native, misfolded, and uncollapsed forms and protein aggregates. Misfolded and uncollapased proteins are the "nucleus" of the aggregates that also encapsulate some correctly folded proteins (native proteins). An optimum hydrophobic interaction strength (epsilon*(p)) between the hydrophobic beads of the model protein, which results from a compromise between the kinetics of collapse and rearrangement, is identified for use in increasing the rate of folding over aggregating. Increased protein concentration hinders the structural transitions in both collapse and rearrangement and thus favors aggregation. A new method for protein folding at high concentration is proposed, which uses an oscillatory molecular driving force (epsilon*(p)) to promote the dissociation of aggregates in the low epsilon*(p) regime while promoting folding at a high epsilon*(p). The advantage of this method in enhancing protein folding while depressing aggregation is illustrated by a comparison with the methods based on direct dilution or applying a denaturant gradient.     

Dual-fluorescent donor-acceptor dyad with tercarbazole donor and switchable imide acceptor: promising structure for an integrated logic gate

A dual-fluorescent donor-acceptor (D-A) dyad with tercarbazole (donor) and 2,3-dithienylmaleimide (acceptor) was synthesized and characterized. The emission intensity of long wavelength could be regulated by either bistable structures of the dyad or the polarities of solvents. By mimicking the function of an integrated logic gate, a 2-input AND logic operation is established. [reaction: see text].     

A multianalyte chemosensor on a single molecule: promising structure for an integrated logic gate

A novel fluorescent probe that possess both BODIPY and Rhodamine moieties has been designed for the selective detection of Hg(2+) and Ba(2+) ions on the controlling by a logic gate. The characteristic fluorescence of the Ba(2+)-selective OFF-ON and the Hg(2+)-selective fluorescence bathochromic shift can be observed, and the concept has been used to construct a combinational logic circuit at the molecular level. These results will be useful for further molecular design to mimic the function of the complex logic gates on controlling.